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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs121913663

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:24956098 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000011 (3/264690, TOPMED)
T=0.000014 (2/140304, GnomAD)
T=0.00002 (2/94122, ExAC) (+ 2 more)
A=0.00003 (1/35878, ALFA)
T=0.00003 (1/35878, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NEFL : Stop Gained
Publications
1 citation
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 51472 C=0.99992 A=0.00002, T=0.00006
European Sub 36122 C=0.99994 A=0.00000, T=0.00006
African Sub 8046 C=0.9999 A=0.0001, T=0.0000
African Others Sub 292 C=1.000 A=0.000, T=0.000
African American Sub 7754 C=0.9999 A=0.0001, T=0.0000
Asian Sub 112 C=1.000 A=0.000, T=0.000
East Asian Sub 86 C=1.00 A=0.00, T=0.00
Other Asian Sub 26 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 496 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 628 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 5970 C=0.9998 A=0.0000, T=0.0002


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999989 T=0.000011
gnomAD - Genomes Global Study-wide 140304 C=0.999986 T=0.000014
gnomAD - Genomes European Sub 75968 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 42064 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13666 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 94122 C=0.99998 T=0.00002
ExAC Europe Sub 57126 C=0.99996 T=0.00004
ExAC Asian Sub 20646 C=1.00000 T=0.00000
ExAC American Sub 9280 C=1.0000 T=0.0000
ExAC African Sub 6400 C=1.0000 T=0.0000
ExAC Other Sub 670 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 35878 C=0.99994 A=0.00003, T=0.00003
Allele Frequency Aggregator European Sub 26562 C=0.99996 A=0.00000, T=0.00004
Allele Frequency Aggregator Other Sub 4640 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 3342 C=0.9997 A=0.0003, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 496 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, T=0.00
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 8 NC_000008.11:g.24956098C>A
GRCh38.p14 chr 8 NC_000008.11:g.24956098C>T
GRCh37.p13 chr 8 NC_000008.10:g.24813612C>A
GRCh37.p13 chr 8 NC_000008.10:g.24813612C>T
NEFL RefSeqGene (LRG_259) NG_008492.1:g.5520G>T
NEFL RefSeqGene (LRG_259) NG_008492.1:g.5520G>A
Gene: NEFL, neurofilament light chain (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NEFL transcript NM_006158.5:c.418G>T E [GAG] > * [TAG] Coding Sequence Variant
neurofilament light polypeptide NP_006149.2:p.Glu140Ter E (Glu) > * (Ter) Stop Gained
NEFL transcript NM_006158.5:c.418G>A E [GAG] > K [AAG] Coding Sequence Variant
neurofilament light polypeptide NP_006149.2:p.Glu140Lys E (Glu) > K (Lys) Missense Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: A (allele ID: 29073 )
ClinVar Accession Disease Names Clinical Significance
RCV000015079.27 Charcot-Marie-Tooth disease type 1F Pathogenic
RCV000057137.1 not provided Not-Provided
Allele: T (allele ID: 567738 )
ClinVar Accession Disease Names Clinical Significance
RCV000688624.1 Charcot-Marie-Tooth disease type 2E Uncertain-Significance
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= A T
GRCh38.p14 chr 8 NC_000008.11:g.24956098= NC_000008.11:g.24956098C>A NC_000008.11:g.24956098C>T
GRCh37.p13 chr 8 NC_000008.10:g.24813612= NC_000008.10:g.24813612C>A NC_000008.10:g.24813612C>T
NEFL RefSeqGene (LRG_259) NG_008492.1:g.5520= NG_008492.1:g.5520G>T NG_008492.1:g.5520G>A
NEFL transcript NM_006158.5:c.418= NM_006158.5:c.418G>T NM_006158.5:c.418G>A
NEFL transcript NM_006158.4:c.418= NM_006158.4:c.418G>T NM_006158.4:c.418G>A
neurofilament light polypeptide NP_006149.2:p.Glu140= NP_006149.2:p.Glu140Ter NP_006149.2:p.Glu140Lys
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

8 SubSNP, 6 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss275515616 Nov 24, 2010 (133)
2 HIFD-CURATED-RECORDS ss538292527 Jul 31, 2012 (137)
3 EVA_EXAC ss1689135797 Apr 01, 2015 (144)
4 GNOMAD ss2737059747 Nov 08, 2017 (151)
5 GNOMAD ss2748019574 Nov 08, 2017 (151)
6 GNOMAD ss2864543700 Nov 08, 2017 (151)
7 ILLUMINA ss3726524539 Jul 13, 2019 (153)
8 TOPMED ss4779462045 Apr 26, 2021 (155)
9 ExAC NC_000008.10 - 24813612 Oct 12, 2018 (152)
10 gnomAD - Genomes NC_000008.11 - 24956098 Apr 26, 2021 (155)
11 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6229339 (NC_000008.10:24813611:C:C 236425/236426, NC_000008.10:24813611:C:A 1/236426)
Row 6229340 (NC_000008.10:24813611:C:C 236425/236426, NC_000008.10:24813611:C:T 1/236426)

- Jul 13, 2019 (153)
12 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6229339 (NC_000008.10:24813611:C:C 236425/236426, NC_000008.10:24813611:C:A 1/236426)
Row 6229340 (NC_000008.10:24813611:C:C 236425/236426, NC_000008.10:24813611:C:T 1/236426)

- Jul 13, 2019 (153)
13 TopMed NC_000008.11 - 24956098 Apr 26, 2021 (155)
14 ALFA NC_000008.11 - 24956098 Apr 26, 2021 (155)
15 ClinVar RCV000015079.27 Oct 12, 2018 (152)
16 ClinVar RCV000057137.1 Oct 12, 2018 (152)
17 ClinVar RCV000688624.1 Jul 13, 2019 (153)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2737059747 NC_000008.10:24813611:C:A NC_000008.11:24956097:C:A (self)
RCV000015079.27, RCV000057137.1, 9261554465, ss275515616, ss538292527, ss3726524539 NC_000008.11:24956097:C:A NC_000008.11:24956097:C:A (self)
9231142, ss1689135797, ss2737059747, ss2748019574, ss2864543700 NC_000008.10:24813611:C:T NC_000008.11:24956097:C:T (self)
RCV000688624.1, 290350690, 616839605, 9261554465, ss4779462045 NC_000008.11:24956097:C:T NC_000008.11:24956097:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs121913663
PMID Title Author Year Journal
19158810 Neurofilament light chain polypeptide gene mutations in Charcot-Marie-Tooth disease: nonsense mutation probably causes a recessive phenotype. Abe A et al. 2009 Journal of human genetics
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07